Methods and apparatus for accurate and efficient sequencing of biomolecules, such as DNA, RNA, and proteins have long been sought. Knowledge of the exact sequence of biomolecules can be used in the search for cures for diseases and other ailments. Prior methods, however, have failed to provide desirable accuracy and throughput rates. In many applications such as diagnostic medicine and bio-defense, it is possible or even desirable to uniquely identify biomolecules without knowledge of every base-pair (i.e. complete sequencing data).